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Gan P, Hajis MIB, Yumna M, Haruman J, Matoha HK, Wahyudi DT, Silalahi S, Oktariani DR, Dela F, Annisa T, Pitaloka TDA, Adhiwijaya PK, Pauzi RY, Hertanto R, Kumaheri MA, Sani L, Irwanto A, Pradipta A, Chomchopbun K, Gonzalez-Porta M. Development and validation of a pharmacogenomics reporting workflow based on the illumina global screening array chip. Front Pharmacol 2024; 15:1349203. [PMID: 38529185 PMCID: PMC10961362 DOI: 10.3389/fphar.2024.1349203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/27/2024] Open
Abstract
Background: Microarrays are a well-established and widely adopted technology capable of interrogating hundreds of thousands of loci across the human genome. Combined with imputation to cover common variants not included in the chip design, they offer a cost-effective solution for large-scale genetic studies. Beyond research applications, this technology can be applied for testing pharmacogenomics, nutrigenetics, and complex disease risk prediction. However, establishing clinical reporting workflows requires a thorough evaluation of the assay's performance, which is achieved through validation studies. In this study, we performed pre-clinical validation of a genetic testing workflow based on the Illumina Global Screening Array for 25 pharmacogenomic-related genes. Methods: To evaluate the accuracy of our workflow, we conducted multiple pre-clinical validation studies. Here, we present the results of accuracy and precision assessments, involving a total of 73 cell lines. These assessments encompass reference materials from the Genome-In-A-Bottle (GIAB), the Genetic Testing Reference Material Coordination Program (GeT-RM) projects, as well as additional samples from the 1000 Genomes project (1KGP). We conducted an accuracy assessment of genotype calls for target loci in each indication against established truth sets. Results: In our per-sample analysis, we observed a mean analytical sensitivity of 99.39% and specificity 99.98%. We further assessed the accuracy of star-allele calls by relying on established diplotypes in the GeT-RM catalogue or calls made based on 1KGP genotyping. On average, we detected a diplotype concordance rate of 96.47% across 14 pharmacogenomic-related genes with star allele-calls. Lastly, we evaluated the reproducibility of our findings across replicates and observed 99.48% diplotype and 100% phenotype inter-run concordance. Conclusion: Our comprehensive validation study demonstrates the robustness and reliability of the developed workflow, supporting its readiness for further development for applied testing.
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Affiliation(s)
- Pamela Gan
- Nalagenetics Pte Ltd., Singapore, Singapore
| | | | | | | | | | | | | | | | - Fitria Dela
- PT Genomik Solidaritas Indonesia, Jakarta, Indonesia
| | - Tazkia Annisa
- PT Genomik Solidaritas Indonesia, Jakarta, Indonesia
| | | | | | | | | | | | | | | | - Ariel Pradipta
- PT Genomik Solidaritas Indonesia, Jakarta, Indonesia
- Department Biochemistry and Molecular Biology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
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2
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Kanji CR, Mbavha BT, Masimirembwa C, Thelingwani RS. Analytical validation of GenoPharm a clinical genotyping open array panel of 46 pharmacogenes inclusive of variants unique to people of African ancestry. PLoS One 2023; 18:e0292131. [PMID: 37788265 PMCID: PMC10547200 DOI: 10.1371/journal.pone.0292131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023] Open
Abstract
Pharmacogenomic testing may be used to improve treatment outcomes and reduce the frequency of adverse drug reactions (ADRs). Population specific, targeted pharmacogenetics (PGx) panel-based testing methods enable sensitive, accurate and economical implementation of precision medicine. We evaluated the analytical performance of the GenoPharm® custom open array platform which evaluates 120 SNPs across 46 pharmacogenes. Using commercially available reference samples (Coriell Biorepository) and in-house extracted DNA, we assessed accuracy, precision, and linearity of GenoPharm®. We then used GenoPharm® on 218 samples from two Southern African black populations and determined allele and genotype frequencies for selected actionable variants. Across all assays, the GenoPharm® panel demonstrated 99.5% concordance with the Coriell reference samples, with 98.9% reproducibility. We observed high frequencies of key genetic variants in people of African ancestry: CYP2B6*6 (0.35), CYP2C9*8, *11 (0.13, 0.03), CYP2D6*17 (0.21) and *29 (0.11). GenoPharm® open array is therefore an accurate, reproducible and sensitive test that can be used for clinical pharmacogenetic testing and is inclusive of variants specific to the people of African ancestry.
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Affiliation(s)
- Comfort Ropafadzo Kanji
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Beatrice, Zimbabwe
- Department of Clinical Pharmacology, University of Zimbabwe (UZ), Harare, Zimbabwe
| | - Bianza Tinotenda Mbavha
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Beatrice, Zimbabwe
| | - Collen Masimirembwa
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Beatrice, Zimbabwe
| | - Roslyn Stella Thelingwani
- Department of Genomic Medicine, African Institute of Biomedical Science and Technology (AiBST), Beatrice, Zimbabwe
- CradleOmics, Harare, Zimbabwe
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3
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Lezirovitz K, Mingroni-Netto RC. Genetic etiology of non-syndromic hearing loss in Latin America. Hum Genet 2021; 141:539-581. [PMID: 34652575 DOI: 10.1007/s00439-021-02354-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/23/2021] [Indexed: 12/16/2022]
Abstract
Latin America comprises all countries from South and Central America, in addition to Mexico. It is characterized by a complex mosaic of regions with heterogeneous genetic profiles regarding the geographical origin of the ancestors and proportions of admixture between the Native American, European and African components. In the first years following the findings of the role of the GJB2/GJB6 genes in the etiology of hearing loss, most scientific investigations about the genetics of hearing loss in Latin America focused on assessing the frequencies of pathogenic variants in these genes. More recently, modern techniques allowed researchers in Latin America to make exciting contributions to the finding of new candidate genes, novel mechanisms of inheritance in previously known genes, and characterize a wide diversity of variants, many of them unique to Latin America. This review aimed to provide a general landscape of the genetic studies about non-syndromic hearing loss in Latin America and their main scientific contributions. It allows the conclusion that, although there are similar contributions of some genes, such as GJB2/GJB6, when compared to European and North American countries, Latin American populations revealed some peculiarities that indicate the need for tailored strategies of screening and diagnosis to specific geographic regions.
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Affiliation(s)
- Karina Lezirovitz
- Laboratório de Otorrinolaringologia/LIM32, Faculdade de Medicina, Hospital das Clínicas, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Regina Célia Mingroni-Netto
- Departamento de Genética e Biologia Evolutiva, Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Batissoco AC, Pedroso-Campos V, Pardono E, Sampaio-Silva J, Sonoda CY, Vieira-Silva GA, da Silva de Oliveira Longati EU, Mariano D, Hoshino ACH, Tsuji RK, Jesus-Santos R, Abath-Neto O, Bento RF, Oiticica J, Lezirovitz K. Molecular and genetic characterization of a large Brazilian cohort presenting hearing loss. Hum Genet 2021; 141:519-538. [PMID: 34599368 DOI: 10.1007/s00439-021-02372-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/15/2021] [Indexed: 12/16/2022]
Abstract
Hearing loss is one of the most common sensory defects, affecting 5.5% of the worldwide population and significantly impacting health and social life. It is mainly attributed to genetic causes, but their relative contribution reflects the geographical region's socio-economic development. Extreme genetic heterogeneity with hundreds of deafness genes involved poses challenges for molecular diagnosis. Here we report the investigation of 542 hearing-impaired subjects from all Brazilian regions to search for genetic causes. Biallelic GJB2/GJB6 causative variants were identified in 12.9% (the lowest frequency was found in the Northern region, 7.7%), 0.4% carried GJB2 dominant variants, and 0.6% had the m.1555A > G variant (one aminoglycoside-related). In addition, other genetic screenings, employed in selected probands according to clinical presentation and presumptive inheritance patterns, identified causative variants in 2.4%. Ear malformations and auditory neuropathy were diagnosed in 10.8% and 3.5% of probands, respectively. In 3.8% of prelingual/perilingual cases, Waardenburg syndrome was clinically diagnosed, and in 71.4%, these diagnoses were confirmed with pathogenic variants revealed; seven out of them were novel, including one CNV. All these genetic screening strategies revealed causative variants in 16.2% of the cases. Based on causative variants in the molecular diagnosis and genealogy analyses, a probable genetic etiology was found in ~ 50% of the cases. The present study highlights the relevance of GJB2/GJB6 as a cause of hearing loss in all Brazilian regions and the importance of screening unselected samples for estimating frequencies. Moreover, when a comprehensive screening is not available, molecular diagnosis can be enhanced by selecting probands for specific screenings.
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Affiliation(s)
- Ana Carla Batissoco
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
- ENT Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brasil
| | - Vinicius Pedroso-Campos
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Eliete Pardono
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
- Instituto de Ciências de Saúde da UNIP, São Paulo, SP, Brasil
| | - Juliana Sampaio-Silva
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Cindy Yukimi Sonoda
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Gleiciele Alice Vieira-Silva
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | | | - Diego Mariano
- Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
| | - Ana Cristina Hiromi Hoshino
- ENT Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brasil
| | - Robinson Koji Tsuji
- ENT Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brasil
| | - Rafaela Jesus-Santos
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Osório Abath-Neto
- Departamento de Neurologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Ricardo Ferreira Bento
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
- ENT Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brasil
| | - Jeanne Oiticica
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil
- ENT Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brasil
| | - Karina Lezirovitz
- Laboratório de Otorrinolaringologia/LIM 32, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brasil.
- ENT Department, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brasil.
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Tang NY, Pei X, George D, House L, Danahey K, Lipschultz E, Ratain MJ, O'Donnell PH, Yeo KTJ, van Wijk XMR. Validation of a Large Custom-Designed Pharmacogenomics Panel on an Array Genotyping Platform. J Appl Lab Med 2021; 6:1505-1516. [PMID: 34263311 DOI: 10.1093/jalm/jfab056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/07/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND Pharmacogenomics has the potential to improve patient outcomes through predicting drug response. We designed and evaluated the analytical performance of a custom OpenArray® pharmacogenomics panel targeting 478 single-nucleotide variants (SNVs). METHODS Forty Coriell Institute cell line (CCL) DNA samples and DNA isolated from 28 whole-blood samples were used for accuracy evaluation. Genotyping calls were compared to at least 1 reference method: next-generation sequencing, Sequenom MassARRAY®, or Sanger sequencing. For precision evaluation, 23 CCL samples were analyzed 3 times and reproducibility of the assays was assessed. For sensitivity evaluation, 6 CCL samples and 5 whole-blood DNA samples were analyzed at DNA concentrations of 10 ng/µL and 50 ng/µL, and their reproducibility and genotyping call rates were compared. RESULTS For 443 variants, all samples assayed had concordant calls with at least 1 reference genotype and also demonstrated reproducibility. However, 6 of these 443 variants showed an unsatisfactory performance, such as low PCR amplification or insufficient separation of genotypes in scatter plots. Call rates were comparable between 50 ng/µL DNA (99.6%) and 10 ng/µL (99.2%). Use of 10 ng/µL DNA resulted in an incorrect call for a single sample for a single variant. Thus, as recommended by the manufacturer, 50 ng/µL is the preferred concentration for patient genotyping. CONCLUSIONS We evaluated a custom-designed pharmacogenomics panel and found that it reliably interrogated 437 variants. Clinically actionable results from selected variants on this panel are currently used in clinical studies employing pharmacogenomics for clinical decision-making.
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Affiliation(s)
- Nga Yeung Tang
- Department of Pathology, Advanced Technology Clinical Laboratory, The University of Chicago, Chicago, IL
| | - Xun Pei
- Department of Pathology, Advanced Technology Clinical Laboratory, The University of Chicago, Chicago, IL
| | - David George
- Department of Pathology, Advanced Technology Clinical Laboratory, The University of Chicago, Chicago, IL
| | - Larry House
- Department of Pathology, Advanced Technology Clinical Laboratory, The University of Chicago, Chicago, IL
| | - Keith Danahey
- Center for Personalized Therapeutics, The University of Chicago, Chicago, IL.,Center for Research Informatics, The University of Chicago, Chicago, IL
| | - Elizabeth Lipschultz
- Center for Personalized Therapeutics, The University of Chicago, Chicago, IL.,Center for Research Informatics, The University of Chicago, Chicago, IL
| | - Mark J Ratain
- Center for Personalized Therapeutics, The University of Chicago, Chicago, IL.,Department of Medicine, The University of Chicago, Chicago, IL
| | - Peter H O'Donnell
- Center for Personalized Therapeutics, The University of Chicago, Chicago, IL.,Department of Medicine, The University of Chicago, Chicago, IL
| | - Kiang-Teck J Yeo
- Department of Pathology, Advanced Technology Clinical Laboratory, The University of Chicago, Chicago, IL.,Center for Personalized Therapeutics, The University of Chicago, Chicago, IL
| | - Xander M R van Wijk
- Department of Pathology, Advanced Technology Clinical Laboratory, The University of Chicago, Chicago, IL.,Center for Personalized Therapeutics, The University of Chicago, Chicago, IL
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Broggini C, Membrillo A, Carranza J. An open platform system based on SNP type genetic markers for discrimination between Alectoris rufa and Alectoris chukar. Mol Cell Probes 2020; 54:101673. [PMID: 33166632 DOI: 10.1016/j.mcp.2020.101673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 11/02/2020] [Indexed: 10/23/2022]
Abstract
The red-legged partridge (Alectoris rufa) is one of the most emblematic game species in Southern Europe. For the conservation of its natural populations against hybridization with chukar partridges (Alectoris chukar) a public and agreed control system able to detect genetic introgression between the two species should be established. As the already available method has not been implemented yet, this paper presents an improvement of the genetic analysis technique by using an open platform system to optimize the diagnostic procedure. Here we present the results obtained from the design of an Open Array™ platform with the available SNPs with proved diagnosis capacity between the two species of interest. By this procedure we genotyped 380 partridge samples, both from farms and field populations, which resulted in an overall percentage of genotyping performed with success of 99.64%. The Open Array genotyping plates showed high performance, specificity and an easy reproducibility compared to conventional techniques of genotyping.
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Affiliation(s)
- Camilla Broggini
- Wildlife Research Unit (UIRCP-UCO), University of Córdoba, Spain.
| | | | - Juan Carranza
- Wildlife Research Unit (UIRCP-UCO), University of Córdoba, Spain
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7
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Kiseleva AV, Klimushina MV, Sotnikova EA, Divashuk MG, Ershova AI, Skirko OP, Kurilova OV, Zharikova AA, Khlebus EY, Efimova IA, Pokrovskaya MS, Slominsky PA, Shalnova SA, Meshkov AN, Drapkina OM. A Data-Driven Approach to Carrier Screening for Common Recessive Diseases. J Pers Med 2020; 10:E140. [PMID: 32971794 PMCID: PMC7563953 DOI: 10.3390/jpm10030140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022] Open
Abstract
Genetic screening is an advanced tool for reducing recessive disease burden. Nowadays, it is still unclear as to the number of genes or their variants that are necessary for effective screening. This paper describes the development of a carrier screening custom panel for cystic fibrosis, phenylketonuria, alpha-1 antitrypsin deficiency, and sensorineural hearing loss consisting of 116 variants in the CFTR, PAH, SERPINA1, and GJB2 genes. The approach is based on the cheapest and fastest method, on using a small number of genes, and on the estimation of the effectiveness of carriers' detection. The custom panel was tested on a population-based cohort that included 1244 participants. Genotypes were determined by the TaqMan OpenArray Genotyping platform on the QuantStudio 12K Flex Real-Time PCR System. The frequency of heterozygotes in the Russian population was 16.87% or 1:6 (CI95%: 14.76-19.00% by Clopper-Pearson exact method): in CFTR-2.81% (1:36), PAH-2.33% (1:43), SERPINA1-4.90% (1:20), and GJB2-6.83% (1:15). The data on allele frequencies were obtained for the first time on a Russian population. The panel allows us to identify the vast majority of carriers of recessive diseases in the population. It is an effective approach to carrier screening for common recessive diseases.
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Affiliation(s)
- Anna V. Kiseleva
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Marina V. Klimushina
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Evgeniia A. Sotnikova
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Mikhail G. Divashuk
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
- Kurchatov Genomics Center-ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia
| | - Alexandra I. Ershova
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Olga P. Skirko
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Olga V. Kurilova
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Anastasia A. Zharikova
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory, 1-73, 119991 Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bol’shoi Karetnyi per., 19, 127051 Moscow, Russia
| | - Eleonora Yu. Khlebus
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Irina A. Efimova
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Maria S. Pokrovskaya
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Petr A. Slominsky
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq., 2, 123182 Moscow, Russia;
| | - Svetlana A. Shalnova
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Alexey N. Meshkov
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
| | - Oxana M. Drapkina
- National Medical Research Center for Preventive Medicine, Ministry of Healthcare of the Russian Federation, Petroverigsky per., 10, bld. 3, 101000 Moscow, Russia; (M.V.K.); (E.A.S.); (M.G.D.); (A.I.E.); (O.P.S.); (O.V.K.); (A.A.Z.); (E.Y.K.); (I.A.E.); (M.S.P.); (S.A.S.); (A.N.M.); (O.M.D.)
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8
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Bouzaher MH, Worden CP, Jeyakumar A. Systematic Review of Pathogenic GJB2 Variants in the Latino Population. Otol Neurotol 2020; 41:e182-e191. [PMID: 31834214 DOI: 10.1097/mao.0000000000002505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES Define the extent to which GJB2-related hearing loss is responsible for non-syndromic hearing loss (NSHL) in the Latino population. METHODS Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines were followed. PubMed and MEDLINE were accessed from 1966 to 2019 using permutations of the MeSH terms: "Hearing Loss," "Hearing Impairment," "Deafness," "Latin American," "Latino," "GJB2," and "Genetic." Additionally, countries designated as Latino by the US Office of Management and Bureau were cross-referenced as key terms against the aforementioned search criteria. Exclusion criteria included non-English publications, a non-Latino study population, and literature not investigating GJB2. An allele frequency analysis of pathogenic GJB2 variants in the Latino population was performed and stratified by country of origin and reported ethnicity. RESULTS One hundred twenty two unique studies were identified of which 64 met our inclusion criteria. Forty three studies were included in the GJB2 systematic review. A total of 38 pathogenic GJB2 variants were identified across 20 countries in the Latino population. The prevalence of pathogenic GJB2 variants varied by country; however, were generally uncommon with the exception of c.35delG (p.Gly12Valfs*) which displayed an allele frequency of 3.1% in the combined Latino population; ranging from 21% in Colombia to 0% in Guatemala. CONCLUSION Variation in the prevalence of pathogenic GJB2 variants by country likely reflect the heterogeneous nature of ethnic ancestral contributions to the Latino population. Additional research utilizing next generation sequencing might aid in the development of assays for high throughput diagnosis of inherited hearing loss in the multitude of ethnic sub-groups that comprise this and other traditionally marginalized populations.
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Affiliation(s)
| | | | - Anita Jeyakumar
- Division of Otolaryngology, Department of Surgery, Akron Children's Hospital, Akron, Ohio
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9
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Identification and validation of SNP markers linked to seed toxicity in Jatropha curcas L. Sci Rep 2019; 9:10220. [PMID: 31308439 PMCID: PMC6629616 DOI: 10.1038/s41598-019-46698-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 06/05/2019] [Indexed: 12/21/2022] Open
Abstract
Edible/non-toxic varieties of Jatropha curcas L. are gaining increasing attention, providing both oil as biofuel feedstock or even as edible oil and the seed kernel meal as animal feed ingredient. They are a viable alternative to the limitation posed by the presence of phorbol esters in toxic varieties. Accurate genotyping of toxic/non-toxic accessions is critical to breeding management. The aim of this study was to identify SNP markers linked to seed toxicity in J. curcas. For SNP discovery, NGS technology was used to sequence the whole genomes of a toxic and non-toxic parent along with a bulk of 51 toxic and 30 non-toxic F2 plants. To ascertain the association between SNP markers and seed toxicity trait, candidate SNPs were genotyped on 672 individuals segregating for seed toxicity and two collections of J. curcas composed of 96 individuals each. In silico SNP discovery approaches led to the identification of 64 candidate SNPs discriminating non-toxic and toxic samples. These SNPs were mapped on Chromosome 8 within the Linkage Group 8 previously identified as a genomic region important for phorbol ester biosynthesis. The association study identified two new SNPs, SNP_J22 and SNP_J24 significantly linked to low toxicity with R2 values of 0.75 and 0.54, respectively. Our study released two valuable SNP markers for high-throughput, marker-assisted breeding of seed toxicity in J. curcas.
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10
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Yan D, Xiang G, Chai X, Qing J, Shang H, Zou B, Mittal R, Shen J, Smith RJH, Fan YS, Blanton SH, Tekin M, Morton C, Xing W, Cheng J, Liu XZ. Screening of deafness-causing DNA variants that are common in patients of European ancestry using a microarray-based approach. PLoS One 2017; 12:e0169219. [PMID: 28273078 PMCID: PMC5342170 DOI: 10.1371/journal.pone.0169219] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/04/2016] [Indexed: 12/12/2022] Open
Abstract
The unparalleled heterogeneity in genetic causes of hearing loss along with remarkable differences in prevalence of causative variants among ethnic groups makes single gene tests technically inefficient. Although hundreds of genes have been reported to be associated with nonsyndromic hearing loss (NSHL), GJB2, GJB6, SLC26A4, and mitochondrial (mt) MT-RNR1 and MTTS are the major contributors. In order to provide a faster, more comprehensive and cost effective assay, we constructed a DNA fluidic array, CapitalBioMiamiOtoArray, for the detection of sequence variants in five genes that are common in most populations of European descent. They consist of c.35delG, p.W44C, p.L90P, c.167delT (GJB2); 309kb deletion (GJB6); p.L236P, p.T416P (SLC26A4); and m.1555A>G, m.7444G>A (mtDNA). We have validated our hearing loss array by analyzing a total of 160 DNAs samples. Our results show 100% concordance between the fluidic array biochip-based approach and the established Sanger sequencing method, thus proving its robustness and reliability at a relatively low cost.
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Affiliation(s)
- Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Guangxin Xiang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Xingping Chai
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Tsinghua University School of Medicine, Beijing, China
| | - Jie Qing
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Haiqiong Shang
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Bing Zou
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Cambridge, Massachusetts, United States of America
| | - Richard J. H. Smith
- Department of Otolaryngology - Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yao-Shan Fan
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Dr. John T. Macdonald Department of Human Genetics and John P.Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Susan H. Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Mustafa Tekin
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Cynthia Morton
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Evolution and Genomic Science, School of Biological Sciences, Manchester Academic Health Science Center, University of Manchester, United Kingdom
| | - Wanli Xing
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Tsinghua University School of Medicine, Beijing, China
| | - Jing Cheng
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Tsinghua University School of Medicine, Beijing, China
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Tsinghua University School of Medicine, Beijing, China
- Dr. John T. Macdonald Department of Human Genetics and John P.Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
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11
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Manzoli GN, Bademci G, Acosta AX, Félix TM, Cengiz FB, Foster J, Da Silva DSD, Menendez I, Sanchez-Pena I, Tekin D, Blanton SH, Abe-Sandes K, Liu XZ, Tekin M. Targeted Resequencing of Deafness Genes Reveals a Founder MYO15A Variant in Northeastern Brazil. Ann Hum Genet 2016; 80:327-331. [PMID: 27870113 PMCID: PMC5127167 DOI: 10.1111/ahg.12177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 08/23/2016] [Accepted: 10/06/2016] [Indexed: 11/29/2022]
Abstract
Identifying the genetic etiology in a person with hearing loss (HL) is challenging due to the extreme genetic heterogeneity in HL and the population-specific variability. In this study, after excluding GJB2 variants, targeted resequencing of 180 deafness-related genes revealed the causative variants in 11 of 19 (58%) Brazilian probands with autosomal recessive HL. Identified pathogenic variants were in MYO15A (10 families) and CLDN14 (one family). Remarkably, the MYO15A p.(Val1400Met) variant was identified in eight families from the city of Monte Santo in the northeast region of Brazil. Haplotype analysis of this variant was consistent with a single founder. No other cases with this variant were detected among 105 simplex cases from other cities of northeastern Brazil, suggesting that this variant is confined to a geographical region. This study suggests that it is feasible to develop population-specific screening for deafness variants once causative variants are identified in different geographical groups.
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Affiliation(s)
- Gabrielle N Manzoli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Guney Bademci
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Angelina X Acosta
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Têmis M Félix
- Serviço de Genética Médica, Hospital de Clinicas de Porto Alegre, Brazil
| | - F Basak Cengiz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Joseph Foster
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Danniel S Dias Da Silva
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Ibis Menendez
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Isalis Sanchez-Pena
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Demet Tekin
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Susan H Blanton
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Kiyoko Abe-Sandes
- Gonçalo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil
| | - Xue Zhong Liu
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
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12
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Liu Z, Zhang P, He X, Liu S, Tang S, Zhang R, Wang X, Tan J, Peng B, Jiang L, Hong S, Zou L. New multiplex real-time PCR approach to detect gene mutations for spinal muscular atrophy. BMC Neurol 2016; 16:141. [PMID: 27534852 PMCID: PMC4989483 DOI: 10.1186/s12883-016-0651-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 07/29/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is the most common autosomal recessive disease in children, and the diagnosis is complicated and difficult, especially at early stage. Early diagnosis of SMA is able to improve the outcome of SMA patients. In our study, Real-time PCR was developed to measure the gene mutation or deletion of key genes for SMA and to further analyse genotype-phenotype correlation. METHODS The multiple real-time PCR for detecting the mutations of survival of motor neuron (SMN), apoptosis inhibitory protein (NAIP) and general transcription factor IIH, polypeptide 2 gene (GTF2H2) was established and confirmed by DNA sequencing and multiplex ligation-dependent probe amplification (MLPA). The diagnosis and prognosis of 141 hospitalized children, 100 normal children and further 2000 cases of dry blood spot (DBS) samples were analysed by this multiple real-time PCR. RESULTS The multiple real-time PCR was established and the accuracy of it to detect the mutations of SMN, NAIP and GTF2H2 was at least 98.8 % comparing with DNA sequencing and MLPA. Among 141 limb movement disorders children, 75 cases were SMA. 71 cases of SMA (94.67 %) were with SMN c.840 mutation, 9 cases (12 %) with NAIP deletion and 3 cases (4 %) with GTF2H2 deletion. The multiple real-time PCR was able to diagnose and predict the prognosis of SMA patients. Simultaneously, the real-time PCR was applied to detect trace DNA from DBS and able to make an early diagnosis of SMA. CONCLUSION The clinical and molecular characteristics of SMA in Southwest of China were presented. Our work provides a novel way for detecting SMA in children by using real-time PCR and the potential usage in newborn screening for early diagnosis of SMA.
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Affiliation(s)
- Zhidai Liu
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Penghui Zhang
- Center for Clinical Laboratory, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Xiaoyan He
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Shan Liu
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Shi Tang
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Rong Zhang
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Xinbin Wang
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Junjie Tan
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Bin Peng
- Department of Health Statistics, School of Public Health, Chongqing Medical University, Yuzhong District, Chongqing, China
| | - Li Jiang
- Department of Neurology, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Siqi Hong
- Department of Neurology, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Lin Zou
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China. .,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China. .,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China.
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13
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Núñez-Batalla F, Jáudenes-Casaubón C, Sequí-Canet JM, Vivanco-Allende A, Zubicaray-Ugarteche J. 2014 CODEPEH Recommendations: Early Detection of Late Onset Deafness, Audiological Diagnosis, Hearing Aid Fitting and Early Intervention. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2016. [DOI: 10.1016/j.otoeng.2015.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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2014 CODEPEH recommendations: Early detection of late onset deafness, audiological diagnosis, hearing aid fitting and early intervention. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2015; 67:45-53. [PMID: 26443498 DOI: 10.1016/j.otorri.2015.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 05/13/2015] [Accepted: 05/17/2015] [Indexed: 11/23/2022]
Abstract
The latest scientific literature considers early diagnosis of deafness as the key element to define the educational and inclusive prognosis of the deaf child, because it allows taking advantage of the critical period of development (0-4 years). Highly significant differences exist between deaf people who have been stimulated early and those who have received late or improper intervention. Early identification of late-onset disorders requires special attention and knowledge on the part of every childcare professional. Programs and additional actions beyond neonatal screening should be designed and planed to ensure that every child with a significant hearing loss is detected early. For this purpose, the CODEPEH would like to highlight the need for continuous monitoring of children's auditory health. Consequently, CODEPEH has drafted the recommendations included in the present document.
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15
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Pozzi A, Previtali C, Cenadelli S, Gandini L, Galli A, Bongioni G. Genetic traceability of cattle using an OpenArray genotyping platform. Anim Genet 2015; 47:133-4. [PMID: 26427605 DOI: 10.1111/age.12359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Anna Pozzi
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Loc. La Quercia, 26027, Rivolta d'Adda, CR, Italy
| | - Cristina Previtali
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Loc. La Quercia, 26027, Rivolta d'Adda, CR, Italy
| | - Silvia Cenadelli
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Loc. La Quercia, 26027, Rivolta d'Adda, CR, Italy
| | - Luca Gandini
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Loc. La Quercia, 26027, Rivolta d'Adda, CR, Italy
| | - Andrea Galli
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Loc. La Quercia, 26027, Rivolta d'Adda, CR, Italy.,Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero Casearie (CRA-FLC), Viale Piacenza 29, 26900, Lodi, Italy
| | - Graziella Bongioni
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Loc. La Quercia, 26027, Rivolta d'Adda, CR, Italy
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Svidnicki MCCM, Silva-Costa SM, Ramos PZ, dos Santos NZP, Martins FTA, Castilho AM, Sartorato EL. Screening of genetic alterations related to non-syndromic hearing loss using MassARRAY iPLEX® technology. BMC MEDICAL GENETICS 2015; 16:85. [PMID: 26399936 PMCID: PMC4581412 DOI: 10.1186/s12881-015-0232-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 09/15/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Recent advances in molecular genetics have enabled to determine the genetic causes of non-syndromic hearing loss, and more than 100 genes have been related to the phenotype. Due to this extraordinary genetic heterogeneity, a large percentage of patients remain without any molecular diagnosis. This condition imply the need for new methodological strategies in order to detect a greater number of mutations in multiple genes. In this work, we optimized and tested a panel of 86 mutations in 17 different genes screened using a high-throughput genotyping technology to determine the molecular etiology of hearing loss. METHODS The technology used in this work was the MassARRAY iPLEX® platform. This technology uses silicon chips and DNA amplification products for accurate genotyping by mass spectrometry of previous reported mutations. The generated results were validated using conventional techniques, as direct sequencing, multiplex PCR and RFLP-PCR. RESULTS An initial genotyping of control subjects, showed failures in 20 % of the selected alterations. To optimize these results, the failed tests were re-designed and new primers were synthesized. Then, the specificity and sensitivity of the panel demonstrated values above 97 %. Additionally, a group of 180 individuals with NSHL without a molecular diagnosis was screened to test the diagnostic value of our panel, and mutations were identified in 30 % of the cases. In 20 % of the individuals, it was possible to explain the etiology of the HL. Mutations in GJB2 gene were the most prevalent, followed by other mutations in in SLC26A4, CDH23, MT-RNR1, MYO15A, and OTOF genes. CONCLUSIONS The MassARRAY technology has the potential for high-throughput identification of genetic variations. However, we demonstrated that optimization is required to increase the genotyping success and accuracy. The developed panel proved to be efficient and cost-effective, being suitable for applications involving the molecular diagnosis of hearing loss.
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Affiliation(s)
- Maria Carolina Costa Melo Svidnicki
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Sueli Matilde Silva-Costa
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Priscila Zonzini Ramos
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Nathalia Zocal Pereira dos Santos
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Fábio Tadeu Arrojo Martins
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Arthur Menino Castilho
- ENT Department, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Edi Lúcia Sartorato
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
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